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method added: getEventStringsWithCounts() 

Returns list of Pairs <String,Integer>, where each pair consists of a unique indel event observed at the site and the total number of observations of that event. String representation for insertions is verbose (e.g. +ACT), while deletions are represented as "5D" (since read backed pileup has no reference information, so we can not get actual sequence of deleted bases)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2479 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-29 22:41:58 +00:00
parent cf3e59eb4a
commit 8330058216
1 changed files with 30 additions and 2 deletions
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32
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
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@ -2,8 +2,7 @@ package org.broadinstitute.sting.utils.pileup;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.gatk.iterators.IterableIterator;
import org.broadinstitute.sting.utils.Pair;
import java.util.*;
@ -290,6 +289,35 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
return v;
}
public List<Pair<String,Integer>> getEventStringsWithCounts() {
Map<String, Integer> events = new HashMap<String,Integer>();
for ( ExtendedEventPileupElement e : this ) {
Integer cnt;
String indel = null;
switch ( e.getType() ) {
case INSERTION:
indel = "+"+e.getEventBases();
break;
case DELETION:
indel = Integer.toString(e.getEventLength())+"D";
break;
case NOEVENT: continue;
default: throw new StingException("Unknown event type encountered: "+e.getType());
}
cnt = events.get(indel);
if ( cnt == null ) events.put(indel,1);
else events.put(indel,cnt.intValue()+1);
}
List<Pair<String,Integer>> eventList = new ArrayList<Pair<String,Integer>>(events.size());
for ( Map.Entry<String,Integer> m : events.entrySet() ) {
eventList.add( new Pair<String,Integer>(m.getKey(),m.getValue()));
}
return eventList;
}
/**
* Get an array of the mapping qualities